|
Size: 1603
Comment: note on using fixup_mni_perl_path
|
Size: 1806
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| [wiki:Self:DownloadAndInstall top] | [wiki:Self:Installation previous] | [wiki:Self:SetupConfiguration next] | [[DownloadAndInstall|top]] | [[Installation|previous]] | [[SetupConfiguration|next]] |
| Line 11: | Line 11: |
| replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file. | replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file. |
| Line 15: | Line 15: |
| The tar.gz file will extract to a directory called 'freesurfer'. To install, mv the tar.gz file to whereever you wish to install freesurfer, and type: |
The tar.gz file will extract to a directory called 'freesurfer'. Installing into the directory {{{/usr/local}}} is recommended. To install, mv the tar.gz file to whereever you wish to install freesurfer (in this example {{{/usr/local}}}) and type: |
| Line 18: | Line 18: |
| tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz | tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz |
| Line 22: | Line 22: |
| == MINC toolkit perl path fix-up == Some of the MNI tools currently contain hard-coded paths to perl. To fix this situation, type: |
Note that for this installation example, your FREESURFER_HOME becomes: |
| Line 26: | Line 24: |
| fixup_mni_perl_path | export FREESURFER_HOME=/usr/local/freesurfer |
| Line 29: | Line 27: |
| Now the MNI tools will find the perl binary on your platform. You can confirm this by typing 'nu_correct', which should return version information (v1.10). | If you are using tcsh, run this command instead: {{{ setenv FREESURFER_HOME /usr/local/freesurfer }}} Reminder to NMR Center users! [[InternalFreeSurferDistributions|You already have FreeSurfer installed on your system!]] |
| Line 33: | Line 36: |
| A license file is required to enable the tools. One can be | A license file is required to enable the tools. One can be |
| Line 36: | Line 39: |
| http://surfer.nmr.mgh.harvard.edu/registration.html | https://surfer.nmr.mgh.harvard.edu/registration.html |
| Line 39: | Line 42: |
| lines of the license information to a file named .license (thats DOT license) and copy that file to your $FREESURFER_HOME. |
lines of the license information to a file named license.txt and copy that file to your $FREESURFER_HOME. |
| Line 43: | Line 45: |
Next: [wiki:Self:SetupConfiguration setup and configure FreeSurfer]. |
If you came from the Quick Install page, return to that [[QuickInstall|here]].<<BR>> Otherwise, go to this page to [[SetupConfiguration|setup and configure FreeSurfer]]. |
FreeSurfer Linux Installation
Viewing contents
To view the contents of a distribution, once downloaded, type:
tar tzf freesurfer-Linux-<platform>-<release>-full.tar.gz
replacing <platform>-<release> with whatever is appropriate. The 'tar tzf' command will not install the contents, just show the contents of the tar.gz file.
Installing contents
The tar.gz file will extract to a directory called 'freesurfer'. Installing into the directory /usr/local is recommended. To install, mv the tar.gz file to whereever you wish to install freesurfer (in this example /usr/local) and type:
tar -C /usr/local -xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz
Again, replacing <platform>-<release> with your Linux variant.
Note that for this installation example, your FREESURFER_HOME becomes:
export FREESURFER_HOME=/usr/local/freesurfer
If you are using tcsh, run this command instead:
setenv FREESURFER_HOME /usr/local/freesurfer
Reminder to NMR Center users! You already have FreeSurfer installed on your system!
Freesurfer license file
A license file is required to enable the tools. One can be obtained for free by registering at:
https://surfer.nmr.mgh.harvard.edu/registration.html
Upon receiving the license information by email, copy the three lines of the license information to a file named license.txt and copy that file to your $FREESURFER_HOME.
Setup and Configuration
If you came from the Quick Install page, return to that here.
Otherwise, go to this page to setup and configure FreeSurfer.